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Genotype data for single nucleotide polymorphism markers in sporadic breast cancer related genes in a Sri Lankan case-control cohort of postmenopausal women.

ABSTRACT: OBJECTIVE:The data presented herein represents the raw genotype data of a recently conducted larger study which investigated the association of single nucleotide polymorphisms (SNPs) in breast cancer related genes with the risk and clinicopathological profiles of sporadic breast cancer among Sri Lankan women. A case-control study design was adopted to conduct SNP marker disease association testing in an existing blood resource obtained from a cohort of Sri Lankan postmenopausal women with clinically phenotyped sporadic breast cancer and healthy postmenopausal women. The list of haplotype-tagging SNP markers for genotyping was selected based on information available in the published literature and use of bioinformatics tools and databases. Genotyping of 57 selected SNPs in 36 breast cancer related genes was performed using the iPLEX Sequenom Mass-Array platform. DATA DESCRIPTION:The raw genotype data for the 57 SNPs genotyped in 350 women with breast cancer and 350 healthy women are presented in this article. This data might be relevant to other researchers involved in investigating the role of SNPs in breast cancer related genes with the risk of sporadic breast cancer in South Asian populations.

SUBMITTER: Sirisena ND

PROVIDER: S-EPMC6642519 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Genotype data for single nucleotide polymorphism markers in sporadic breast cancer related genes in a Sri Lankan case-control cohort of postmenopausal women.

Sirisena Nirmala Dushyanthi ND Samaranayake Nilakshi N Dissanayake Vajira H W VHW

BMC research notes 20190719 1

<h4>Objective</h4>The data presented herein represents the raw genotype data of a recently conducted larger study which investigated the association of single nucleotide polymorphisms (SNPs) in breast cancer related genes with the risk and clinicopathological profiles of sporadic breast cancer among Sri Lankan women. A case-control study design was adopted to conduct SNP marker disease association testing in an existing blood resource obtained from a cohort of Sri Lankan postmenopausal women wit ...[more]

PMID: 31324265

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Project description:PurposeSeveral single nucleotide polymorphisms (SNPs) have been reported to be associated with clinicopathological profiles in sporadic breast cancer based on studies conducted on major population groups. The knowledge of the effects of these common genetic variants in South Asian populations remains limited. The present study aimed to investigate the association between a selected set of SNPs and the clinicopathological profiles in sporadic breast cancer in Sri Lankan women.MethodsA total of 350 postmenopausal women with histologically confirmed invasive breast cancer were genotyped for 58 SNPs located in 36 breast cancer related genes. The clinicopathological factors that were investigated included age of onset, tumor histologic grade, and lymph node involvement, as well as estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2 (HER2) status. Association testing was performed using logistic regression models adjusted for confounding factors.ResultsSeven SNPs showed significant associations with clinicopathological profiles in breast cancer. The G allele of BRCA1:rs799917 (p=0.047; β [standard error; SE]=-1.069 [0.537]) and the G allele of NQO2:rs17136117 (p=0.040, β [SE]=1.901 [0.923]) were found to be associated with age of onset between 50 and 59 years. The C allele of CDH1:rs13689 (odds ratio [OR], 2.121; p=0.033) was found to be associated with ER-positive breast cancer. The A allele of AKT1:rs1130214 (OR, 2.095; p=0.011) and the C allele of NQO2:rs2071002 (OR, 1.632; p=0.045) were associated with HER2-positive breast cancer. The C allele of BRCA2:rs15869 (OR, 1.600; p=0.041) and the C allele of CCND1:rs7177 (OR, 1.555; p=0.041) were associated with high tumor histologic grade.ConclusionThe common genetic variants identified in the AKT1, BRCA1, BRCA2, CCND1, CDH1, and NQO2 genes could serve as potential clinical and prognostic biomarkers in sporadic breast cancer patients. Further studies are required to validate our current findings in other populations.

Project description:BackgroundBreast cancer and its treatment imposes a significant effect in the quality of life (QOL) of women. Being a developing country with contrasting social and cultural norms to the West, Sri Lankan women may have a different experience on QOL following surgical treatment of breast cancer. This study was conducted to evaluate post-treatment QOL in breast cancer patients and to determine its association with the type of surgery.MethodsA cross sectional study was carried out. Fifty four women with non-metastatic breast cancer who underwent surgery for breast cancer at the Professorial Surgical Unit, Colombo during 2015-2018 and completed a minimum of one year follow up after surgery were invited to participate. Fifty-four women who responded were assessed using the validated EORTC QLQ-C30 and QLQ-BR23 questionnaires. Non-parametric tests were used for statistical analyses.ResultsThe mean age was 59 years (range 36-81). A majority (61%, n = 35) underwent mastectomy and the rest (n = 19, 45%) breast conservation surgery (BCS). The mean QLQ-C30 score was 68.8 (range 8.3-100) and the mean scores for physical function, role function, emotional function, cognitive function, and social function were 71.4, 81.5, 77.0, 80.2, and 86.4, respectively. The mean scores for body image, sexual functioning, sexual enjoyment, future perspective, systemic therapy, breast symptoms, arm symptoms, and hair loss assessed by the QLQ-BR23 were 76.4, 18.3, 33.3, 73.6, 30.5, 16.2, 23.4 and 32.7, respectively. No significant differences (P > 0.05) were noted in global health status, physical function, role function, emotional function, cognitive function and social function between BCS and mastectomy. QLQ-BR23 body image, sexual functioning, sexual enjoyment and future perspective also did not differ significantly (p > 0.05) between the two groups.ConclusionsSexual functioning and enjoyment, breast and arm symptoms and hair loss contributed to poor QOL while the impact on global health status including physical, social and emotional functions were minimal. Type of surgery did not appear to be associated with QOL. Future studies with a larger sample sizes will be helpful to further study these factors.

Project description:Polycystic ovary syndrome (PCOS) is the commonest endocrine disorder affecting women of reproductive age. Its aetiology, though yet unclear, is presumed to have an oligogenic basis interacting with environmental factors. Kisspeptins are peptide products of Kiss1 gene that control the hypothalamic pituitary (HPG) axis by acting via G protein-coupled receptor known as GPR54. There is paucity of data on the role of Kiss1 and GPR54 gene in PCOS. We aimed to identify the polymorphisms in Kiss1 and GPR54 genes and explore their association with serum kisspeptin levels among Sri Lankan women with well-characterized PCOS. Consecutive women with PCOS manifesting from adolescence (n=55) and adult controls (n=110) were recruited. Serum kisspeptin and testosterone levels were determined by ELISA method. Whole gene sequencing was performed to identify the polymorphisms in Kiss1 and GPR54 genes. Serum kisspeptin and testosterone concentrations were significantly higher in women with PCOS than controls: kisspeptin 4.873nmol/L versus 4.127nmol/L; testosterone 4.713nmol/L versus 3.415 nmol/L, p<0.05. Sequencing the GPR54 gene revealed 5 single nucleotide polymorphisms (SNPs), rs10407968, rs1250729403, rs350131, chr19:918686, and chr19:918735, with two novel SNPs (chr19:918686 and chr19:918735), while sequencing the Kiss1 gene revealed 2 SNPs, rs5780218 and rs4889. All identified SNPs showed no significant difference in frequency between patients and controls. GPR54 gene rs350131 polymorphism (G/T) was detected more frequently in our study population. The heterozygous allele (AG) of GPR54 gene novel polymorphism chr19:918686 showed a marginal association with serum kisspeptin levels (p=0.053). Genetic variations in GPR54 and Kiss1 genes are unlikely to be associated with PCOS among Sri Lankan women manifesting from adolescence. Meanwhile the heterozygous allele of chr19:918686 is probably associated with serum kisspeptin concentrations, which suggests a potential role in the aetiology of PCOS.

Dataset Information

Genotype data for single nucleotide polymorphism markers in sporadic breast cancer related genes in a Sri Lankan case-control cohort of postmenopausal women.

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Genotype data for single nucleotide polymorphism markers in sporadic breast cancer related genes in a Sri Lankan case-control cohort of postmenopausal women.

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